System, method, and product for scanning of biological materials

• US 7,983,467 B2
• Filed: 02/11/2010
• Issued: 07/19/2011
• Est. Priority Date: 03/15/2002
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Oleink-Ovod, Ksenia, Weiner, Nathan K., Miles, Christopher, Schultz, Eric, Bukys, Albert, Katz, Joel M., Bradbury, David, DiPaolo, Roger, Odoy, Patrick J., Stura, David A., Regan, Thomas P., Jones, Mark, McKenzie, Eric Earl, Deweerd, Herman, Overbeck, James, Woolaver, Tim
• Primary Examiner(s): Johns; Andrew W
• Application Number:
  US12/704,350
• Publication Number:
  US 20100142850A1
• Time in Patent Office: 523 Days
• Field of Search: 382/128, 382/129, 382/133, 382/293, 382/294, 382/295
• US Class Current: 382/133
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 21/253 for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates

Abstract

An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Claims

1. A method, comprising the acts of:

receiving a plurality of pixel intensity values based, at least in part, upon detected emissions from a plurality of probe features disposed on a probe array; and

associating each of the pixel intensity values with one or more image pixel positions of a probe array image based, at least in part, upon one or more position correction values.

2. The method of claim 1, wherein:

the probe array image has a position error of plus or minus one pixel or less.

3. The method of claim 1, wherein:

the emissions are responsive, at least in part, to an excitation beam.

4. The method of claim 3, wherein:

the emissions arise from excitation by the excitation beam of one or more fluorescent molecules.

5. The method of claim 3, wherein:

the excitation beam comprises a laser beam.

6. The method of claim 5, wherein:

the laser includes a solid state, diode pumped, frequency doubled Nd;

YAG laser.

7. The method of claim 3, wherein:

the act of receiving the plurality of pixel intensity values is accomplished in a single pass of the excitation beam over a number of contiguous probe features of the plurality of probe features.

8. The method of claim 7, wherein:

the contiguous features comprise a scanning line.

9. The method of claim 7, wherein:

the contiguous features are immediately adjacent features or are separated by non-feature areas of the probe array.

10. The method of claim 1, wherein:

each of the plurality of pixel intensity values is associated with a pixel having a dimension in an x-axis with respect to the probe array of approximately 2.5 μ

m.

11. The method of claim 10, wherein:

the dimension in the x-axis is between about 1.5 μ

m and about 3.0 μ

m.

12. The method of claim 1, wherein:

each of the plurality of probe features has a dimension in an x-axis with respect to the probe array of approximately 18 μ

m.

13. The method of claim 12, wherein:

the dimension on the x-axis is between about 14 μ

m and about 22 μ

m.

14. The method of claim 1, wherein:

each of the plurality of probe features has a dimension in an x-axis with respect to the probe array of approximately 10 μ

m.

15. The method of claim 14, wherein:

the dimension on the x-axis is between about 6 μ

m and about 14 μ

m.

16. The method of claim 1, wherein:

each probe feature is associated with one or more of the plurality of pixel intensity values.

17. The method of claim 1, wherein:

the probe array includes a synthesized array or a spotted array.

18. The method of claim 1, wherein:

the one or more position correction values each includes a horizontal linearity correction value, a vertical linearity correction value, or both.

19. The method of claim 1, wherein:

the act of associating each of the plurality of pixel intensity values with one or more image pixel positions is accomplished by adjusting a received pixel position associated with each of the plurality of pixel intensity values by a number of pixels determined by the one or more position correction values.

20. The method of claim 19, wherein:

the number of pixels includes a fractional value.

21. The method of claim 1, wherein:

the one or more position correction values are based, at least in part, upon one or more reference positions provided by one or more calibration features.

22. The method of claim 21, wherein:

the one or more calibration features comprises an array of features oriented in a horizontal pattern, vertical pattern, or both.

23. The method of claim 1, further comprising the acts of:

translating the probe array a distance along a y-axis with respect to the probe array; and

repeating the steps of receiving, associating, and translating until the probe array image includes pixel intensity values corresponding to each of the plurality of probes disposed on the probe array.

24. The method of claim 23, wherein:

the distance is based, at least in part, on a size of a pixel in the y-axis.

25. The method of claim 24, wherein:

the distance is approximately 2.5 μ

m.

26. The method of claim 24, wherein:

the distance is between about 1.5 μ

m and about 3.0 μ

m.

27. A scanning system, comprising:

one or more detectors constructed and arranged to receive a plurality of pixel intensity values based, at least in part, upon detected emissions from a plurality of probe features disposed on a probe array; and

a corrected image generator constructed and arranged to associate each of the pixel intensity values with one or more image pixel positions of a probe array image based, at least in part, upon one or more position correction values.

28. The scanning system of claim 27, wherein:

the probe array image has a position error of plus or minus one pixel or less.

29. The scanning system of claim 27, wherein:

the emissions are responsive, at least in part, to an excitation beam.

30. The scanning system of claim 29, wherein:

the emissions arise from excitation by the excitation beam of one or more fluorescent molecules.

31. The scanning system of claim 29, wherein:

the excitation beam comprises a laser beam.

32. The scanning system of claim 31, wherein:

the laser includes a solid state, diode pumped, frequency doubled Nd;

YAG laser.

33. The scanning system of claim 29, wherein:

the one or more detectors accomplishes the receiving of the plurality of pixel intensity values in a single pass of the excitation beam over a number of contiguous probe features of the plurality of probe features.

34. The scanning system of claim 33, wherein:

the contiguous features comprise a scanning line.

35. The scanning system of claim 33, wherein:

the contiguous features are immediately adjacent features or are separated by non-feature areas of the probe array.

36. The scanning system of claim 27, wherein:

each of the plurality of pixel intensity values is associated with a pixel having a dimension in an x-axis with respect to the probe array of approximately 2.5 μ

m.

37. The scanning system of claim 36, wherein:

the dimension in the x-axis is between about 1.5 μ

m and about 3.0 μ

m.

38. The scanning system of claim 27, wherein:

each of the plurality of probe features has a dimension in an x-axis with respect to the probe array of approximately 18 μ

m.

39. The scanning system of claim 38, wherein:

the dimension on the x-axis is between about 14 μ

m and about 22 μ

m.

40. The scanning system of claim 27, wherein:

each of the plurality of probe features has a dimension in an x-axis with respect to the probe array of approximately 10 μ

m probe feature.

41. The scanning system of claim 40, wherein:

the dimension on the x-axis is between about 6 μ

m and about 14 μ

m.

42. The scanning system of claim 27, wherein:

each probe feature is associated with one or more of the plurality of pixel intensity values.

43. The scanning system of claim 27, wherein:

the probe array includes a synthesized array or a spotted array.

44. The scanning system of claim 27, wherein:

the one or more position correction values each includes a horizontal linearity correction value, a vertical linearity correction value, or both.

45. The scanning system of claim 27, wherein:

the corrected image generator accomplishes the association of each of the plurality of pixel intensity values with one or more image pixel positions by adjusting a received pixel position associated with each of the plurality of pixel intensity values by a number of pixels determined by the one or more position correction values.

46. The scanning system of claim 45, wherein:

the number of pixels includes a fractional value.

47. The scanning system of claim 27, wherein:

the one or more position correction values are based, at least in part, upon one or more reference positions provided by one or more calibration features.

48. The scanning system of claim 47, wherein:

the one or more calibration features comprises an array of features oriented in a horizontal pattern, vertical pattern, or both.

49. The scanning system of claim 27, further comprising:

a transport frame constructed and arranged to translate the probe array a distance along a y-axis with respect to the probe array ; and

a comparator constructed and arranged to determine a completed probe array image based, at least in part, upon one or more received pixel intensity values corresponding to each of the plurality of probes disposed on the probe array.

50. The scanning system of claim 49, wherein:

the distance is based, at least in part, on a size of a pixel in the y-axis.

51. The scanning system of claim 50, wherein:

the distance is approximately 2.5 μ

m.

52. The scanning system of claim 50, wherein:

the distance is between about 1.5 μ

m and about 3.0 μ

m.

53. The scanning system of claim 49, wherein:

the transport frame is further constructed and arranged to provide a solid hinge flexure.

54. The scanning system of claim 53, wherein:

the solid hinge flexure provides movement in the Z-axis.

55. The scanning system of claim 49, wherein:

the solid hinge flexure has no friction or stiction.